Development of type-specific amplicon schemes for whole-genome sequencing of seasonal human coronaviruses from clinical samples
- 1Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana
- 2Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool
Abstract
Seasonal human coronaviruses (sHCoVs), made up of alpha (HCoV-229E and HCoV-NL63) and betacoronaviruses (HCoV-OC43 and HCoV-HKU1), are endemic respiratory pathogens that have been circulating in human populations for decades. Despite their long-standing presence, their genomic diversity remains poorly characterized. This is mainly due to the limited availability of complete genome sequences, especially for HCoV-HKU1. This study presents a comprehensive molecular epidemiological analysis of sHCoVs in Slovenia over an 11-year period (2012–2022) based on 2,365 typed clinical samples. To close the gap in genomic data, virus-specific primer schemes for amplicon-based whole-genome sequencing of all four sHCoV types were developed and validated. These schemes achieved high genome recovery rates in samples with RNA concentrations exceeding 30 cp/µL (Ct ≈ 32), with the most consistent performance observed for HCoV-229E and HCoV-OC43. For HCoV-NL63 and HCoV-HKU1, comparable genome recovery was observed only at higher RNA concentrations, exceeding 50 cp/µL and 200 cp/µL, respectively. Comparative sequencing using Illumina and Oxford Nanopore Technologies (ONT) platforms showed highly consistent genome coverage and variant detection across all sHCoV types. Importantly, the protocols facilitated successful genome recovery even from archived specimens, underscoring their suitability for both retrospective and prospective genomic surveillance. This study expands the global repository of sHCoV genomes and provides a valuable methodological framework for high-resolution monitoring of their genetic evolution and epidemiological dynamics.
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BibTeX
@article{osep2026development,
title = {{Development of type-specific amplicon schemes for whole-genome sequencing of seasonal human coronaviruses from clinical samples}},
author = {Anja Ošep and Hannah Goldswain and Alen Suljič and Rok Kogoj and Miša Korva and Miroslav Petrovec and Julian A. Hiscox and Tina Uršič},
journal = {Scientific Reports},
year = {2026},
month = jul,
doi = {10.1038/s41598-026-63549-1},
url = {https://doi.org/10.1038/s41598-026-63549-1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Development of type-specific amplicon schemes for whole-genome sequencing of seasonal human coronaviruses from clinical samples
AU - Anja Ošep
AU - Hannah Goldswain
AU - Alen Suljič
AU - Rok Kogoj
AU - Miša Korva
AU - Miroslav Petrovec
AU - Julian A. Hiscox
AU - Tina Uršič
PY - 2026
DA - 2026/07/01
JO - Scientific Reports
DO - 10.1038/s41598-026-63549-1
UR - https://doi.org/10.1038/s41598-026-63549-1
AB - Seasonal human coronaviruses (sHCoVs), made up of alpha (HCoV-229E and HCoV-NL63) and betacoronaviruses (HCoV-OC43 and HCoV-HKU1), are endemic respiratory pathogens that have been circulating in human populations for decades. Despite their long-standing presence, their genomic diversity remains poorly characterized. This is mainly due to the limited availability of complete genome sequences, especially for HCoV-HKU1. This study presents a comprehensive molecular epidemiological analysis of sHCoVs in Slovenia over an 11-year period (2012–2022) based on 2,365 typed clinical samples. To close the gap in genomic data, virus-specific primer schemes for amplicon-based whole-genome sequencing of all four sHCoV types were developed and validated. These schemes achieved high genome recovery rates in samples with RNA concentrations exceeding 30 cp/µL (Ct ≈ 32), with the most consistent performance observed for HCoV-229E and HCoV-OC43. For HCoV-NL63 and HCoV-HKU1, comparable genome recovery was observed only at higher RNA concentrations, exceeding 50 cp/µL and 200 cp/µL, respectively. Comparative sequencing using Illumina and Oxford Nanopore Technologies (ONT) platforms showed highly consistent genome coverage and variant detection across all sHCoV types. Importantly, the protocols facilitated successful genome recovery even from archived specimens, underscoring their suitability for both retrospective and prospective genomic surveillance. This study expands the global repository of sHCoV genomes and provides a valuable methodological framework for high-resolution monitoring of their genetic evolution and epidemiological dynamics.
SN - 2045-2322
ER -